kedro.extras.datasets.biosequence.BioSequenceDataSet¶
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class
kedro.extras.datasets.biosequence.
BioSequenceDataSet
(filepath, load_args=None, save_args=None, credentials=None, fs_args=None)[source]¶ Bases:
kedro.io.core.AbstractDataSet
BioSequenceDataSet
loads and saves data to a sequence file.Example:
from kedro.extras.datasets.biosequence import BioSequenceDataSet from io import StringIO from Bio import SeqIO data = ">Alpha\nACCGGATGTA\n>Beta\nAGGCTCGGTTA\n" raw_data = [] for record in SeqIO.parse(StringIO(data), "fasta"): raw_data.append(record) data_set = BioSequenceDataSet(filepath="ls_orchid.fasta", load_args={"format": "fasta"}, save_args={"format": "fasta"}) data_set.save(raw_data) sequence_list = data_set.load() assert raw_data[0].id == sequence_list[0].id assert raw_data[0].seq == sequence_list[0].seq
Attributes
BioSequenceDataSet.DEFAULT_LOAD_ARGS
BioSequenceDataSet.DEFAULT_SAVE_ARGS
Methods
BioSequenceDataSet.__init__
(filepath[, …])Creates a new instance of BioSequenceDataSet
pointing to a concrete filepath.BioSequenceDataSet.exists
()Checks whether a data set’s output already exists by calling the provided _exists() method. BioSequenceDataSet.from_config
(name, config)Create a data set instance using the configuration provided. BioSequenceDataSet.invalidate_cache
()Invalidate underlying filesystem caches. BioSequenceDataSet.load
()Loads data by delegation to the provided load method. BioSequenceDataSet.release
()Release any cached data. BioSequenceDataSet.save
(data)Saves data by delegation to the provided save method. -
DEFAULT_LOAD_ARGS
= {}¶
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DEFAULT_SAVE_ARGS
= {}¶
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__init__
(filepath, load_args=None, save_args=None, credentials=None, fs_args=None)[source]¶ Creates a new instance of
BioSequenceDataSet
pointing to a concrete filepath.Parameters: - filepath (
str
) – Filepath in POSIX format to sequence file prefixed with a protocol like s3://. If prefix is not provided, file protocol (local filesystem) will be used. The prefix should be any protocol supported byfsspec
. - load_args (
Optional
[Dict
[str
,Any
]]) – Options for parsing sequence files by BiopythonSeqIO.parse()
. - save_args (
Optional
[Dict
[str
,Any
]]) – file format supported by BiopythonSeqIO.write()
. E.g. {“format”: “fasta”}. - credentials (
Optional
[Dict
[str
,Any
]]) – Credentials required to get access to the underlying filesystem. E.g. forGCSFileSystem
it should look like {“token”: None}. - fs_args (
Optional
[Dict
[str
,Any
]]) – Extra arguments to pass into underlying filesystem class constructor (e.g. {“project”: “my-project”} forGCSFileSystem
), as well as to pass to the filesystem’s open method through nested keys open_args_load and open_args_save. Here you can find all available arguments for open: https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.spec.AbstractFileSystem.open All defaults are preserved, except mode, which is set to r when loading and to w when saving.
Note: Here you can find all supported file formats: https://biopython.org/wiki/SeqIO
Return type: None
- filepath (
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exists
()¶ Checks whether a data set’s output already exists by calling the provided _exists() method.
Return type: bool
Returns: Flag indicating whether the output already exists. Raises: DataSetError
– when underlying exists method raises error.
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classmethod
from_config
(name, config, load_version=None, save_version=None)¶ Create a data set instance using the configuration provided.
Parameters: - name (
str
) – Data set name. - config (
Dict
[str
,Any
]) – Data set config dictionary. - load_version (
Optional
[str
]) – Version string to be used forload
operation if the data set is versioned. Has no effect on the data set if versioning was not enabled. - save_version (
Optional
[str
]) – Version string to be used forsave
operation if the data set is versioned. Has no effect on the data set if versioning was not enabled.
Return type: AbstractDataSet
Returns: An instance of an
AbstractDataSet
subclass.Raises: DataSetError
– When the function fails to create the data set from its config.- name (
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load
()¶ Loads data by delegation to the provided load method.
Return type: Any
Returns: Data returned by the provided load method. Raises: DataSetError
– When underlying load method raises error.
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release
()¶ Release any cached data.
Raises: DataSetError
– when underlying release method raises error.Return type: None
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save
(data)¶ Saves data by delegation to the provided save method.
Parameters: data ( Any
) – the value to be saved by provided save method.Raises: DataSetError
– when underlying save method raises error.Return type: None
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